nemar-cli 0.3.7-dev.113 → 0.3.7-dev.118

package/README.md

@@ -372,14 +372,73 @@ graph TB
     REL -->|Archive| DOI
 ```
 
+## Testing
+
+### Running Tests
+
+```bash
+# All tests
+bun test
+
+# Specific test file
+bun test test/cli.test.ts
+bun test test/api.test.ts
+```
+
+### Zenodo Sandbox Tests
+
+DOI workflows can be tested using Zenodo's sandbox environment without affecting production:
+
+```bash
+# Run Zenodo sandbox tests (requires configuration)
+RUN_ZENODO_TESTS=true TEST_DATASET_ID=nm099999 bun test test/zenodo-sandbox.test.ts
+```
+
+**Setup requirements:**
+1. Create account on [sandbox.zenodo.org](https://sandbox.zenodo.org)
+2. Generate API token with `deposit:write` scope
+3. Add to `test/.env.test`:
+   ```bash
+   ZENODO_SANDBOX_API_KEY=your_sandbox_token
+   RUN_ZENODO_TESTS=true
+   TEST_DATASET_ID=nm099999
+   ```
+
+**Test coverage:**
+- Concept DOI creation and retrieval
+- Version DOI publishing workflows
+- Metadata updates (title, keywords, related identifiers)
+- Error handling (401, 404, 400 responses)
+- Rate limiting and request throttling
+- Deposition lifecycle (create → upload → publish)
+- File uploads with checksum verification
+
+See [docs/development/zenodo-testing.md](docs/development/zenodo-testing.md) for comprehensive guide.
+
 ## Environment Variables
 
+### CLI Usage
+
 ```bash
 NEMAR_API_KEY          # API key (alternative to login)
 NEMAR_API_URL          # Custom API endpoint (default: https://api.nemar.org)
 NEMAR_NO_COLOR         # Disable colored output
 ```
 
+### Testing
+
+```bash
+# Required for Zenodo sandbox tests
+ZENODO_SANDBOX_API_KEY # Sandbox Zenodo API token
+RUN_ZENODO_TESTS       # Enable Zenodo tests (set to "true")
+TEST_DATASET_ID        # Test dataset ID (default: nm099999)
+
+# API testing
+TEST_API_URL           # Test API endpoint (dev environment)
+TEST_ADMIN_API_KEY     # Admin API key for tests
+TEST_USER_API_KEY      # User API key for tests
+```
+
 ## Troubleshooting
 
 ### Upload Issues

package/dist/index.js

@@ -145,7 +145,7 @@ ${E.cyan("CI Status:")} ${D}
 `);let B=$.bids_validation.present,J=B?E.green("[x]"):E.red("[ ]");if(console.log(`  ${J} BIDS Validation`),B){let X=$.bids_validation.status==="success"?E.green:$.bids_validation.status==="failure"?E.red:E.yellow;if(console.log(`      Status: ${X($.bids_validation.status)}`),$.bids_validation.url)console.log(`      URL:    ${E.gray($.bids_validation.url)}`)}else console.log(`      ${E.gray("Not deployed. Use 'nemar admin ci add' to deploy.")}`);let Q=$.version_check.present,Y=Q?E.green("[x]"):E.red("[ ]");if(console.log(`  ${Y} Version Check`),!Q)console.log(`      ${E.gray("Not deployed. Use 'nemar admin ci add' to deploy.")}`);console.log()}catch($){if($ instanceof u){if(F.fail($.message),$.statusCode===403)console.log(E.gray("  This command requires admin privileges"));else if($.statusCode===404)console.log(E.gray("  Dataset not found"))}else{F.fail("Failed to check CI status");let B=$ instanceof Error?$.message:String($);console.log(E.gray(`  Error details: ${B}`))}}});C2.command("add").description("Deploy CI workflows to a dataset repository").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option(_D,fD).option(tD,eD).action(async(D,F)=>{if(!w0())return;console.log(E.cyan(`
 Deploy CI workflows to: ${D}
 `)),console.log("This will add the following workflows:"),console.log("  1. BIDS Validation (runs on PRs)"),console.log("  2. Version Check (ensures version bump on PRs)"),console.log("  3. PR Merge Handler (creates releases, publishes DOIs)"),console.log();let $=await rD(`Deploy CI workflows to ${D}?`,F);if($!=="confirmed"){console.log(E.gray($==="declined"?"Skipped":"Cancelled"));return}let B=C(`Deploying CI workflows to ${D}...`).start();try{let J=await K$(D);B.succeed("CI workflows deployed"),console.log();for(let Q of J.workflows_deployed)console.log(`  ${E.green("[x]")} ${Q}`);console.log()}catch(J){if(J instanceof u){if(B.fail(J.message),J.statusCode===403)console.log(E.gray("  This command requires admin privileges"));else if(J.statusCode===404)console.log(E.gray("  Dataset not found"))}else{B.fail("Failed to deploy CI workflows");let Q=J instanceof Error?J.message:String(J);console.log(E.gray(`  Error details: ${Q}`))}}});n0.addCommand(C2);var R2=new D0("doi").description("DOI management");R2.command("create").description("Create concept DOI for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--title <title>","DOI title (defaults to dataset name)").option("--description <desc>","DOI description").option("--sandbox","Use Zenodo sandbox for testing").option(_D,fD).option(tD,eD).action(async(D,F)=>{if(!w0())return;let $=C("Fetching dataset info...").start(),B;try{B=await e8(D),$.succeed(`Found dataset: ${B.name}`)}catch(X){if(X instanceof u){if($.fail(X.message),X.statusCode===404)console.log(E.gray("  Dataset not found"))}else $.fail("Failed to fetch dataset");return}try{let X=await A2(D);if(X.concept_doi){if(console.log(E.yellow(`
-Dataset already has a concept DOI:`)),console.log(`  Concept DOI: ${E.cyan(X.concept_doi)}`),X.zenodo_concept_url)console.log(`  Zenodo URL:  ${X.zenodo_concept_url}`);return}}catch{}if(console.log(),console.log(E.cyan("Dataset Information:")),console.log(`  ID:          ${B.dataset_id}`),console.log(`  Name:        ${B.name}`),B.github_repo)console.log(`  GitHub:      ${B.github_repo}`);if(F.sandbox)console.log(`  Mode:        ${E.yellow("SANDBOX (test DOI)")}`);console.log(),console.log(E.red("WARNING: DOIs are PERMANENT and cannot be deleted!")),console.log(E.gray("The DOI will be pre-reserved but not published until the first version release.")),console.log();let J=F.sandbox?"Create test concept DOI on Zenodo sandbox?":"Create concept DOI on Zenodo?",Q=await rD(J,F);if(Q!=="confirmed"){console.log(E.gray(Q==="declined"?"Skipped":"Cancelled"));return}let Y=C("Creating concept DOI on Zenodo...").start();try{let X=await Cv(D,{title:F.title,description:F.description,sandbox:F.sandbox});Y.succeed("Concept DOI created successfully");let G=C("Applying branch protection...").start();try{let H=await V$(D);if(H.warnings&&H.warnings.length>0){G.warn("Branch protection applied with warnings");for(let W of H.warnings)console.log(E.yellow(`  Warning: ${W}`))}else G.succeed("Branch protection applied")}catch(H){if(G.warn("Could not apply branch protection"),H instanceof u){if(console.log(E.gray(`  ${H.message}`)),H.statusCode===403)console.log(E.gray("  Check admin credentials and permissions"))}else console.log(E.gray(`  ${H instanceof Error?H.message:"Unknown error"}`));console.log(E.gray("  Manual setup: Go to GitHub repo Settings > Branches > Add rule"))}if(console.log(),console.log(E.green("DOI Information:")),console.log(`  Concept DOI: ${E.cyan(X.concept_doi)}`),console.log(`  Zenodo URL:  ${X.zenodo_url}`),console.log(),console.log(E.yellow("Next steps:")),console.log("  1. Set up automatic DOI publishing by running:"),console.log(E.gray(`     ${X.setup_command}`)),console.log("     (paste the webhook token when prompted)"),console.log(),console.log("  2. Update dataset_description.json with DatasetDOI field"),console.log("  3. Create a PR and merge it to trigger version DOI publication"),console.log(),F.sandbox)console.log(E.gray("Note: This is a sandbox DOI and will not resolve in production."))}catch(X){if(X instanceof u){if(Y.fail(X.message),X.statusCode===403)console.log(E.gray("  This command requires admin privileges"))}else Y.fail("Failed to create concept DOI"),console.log(E.gray(`  ${X instanceof Error?X.message:"Unknown error"}`))}});R2.command("info").description("Get DOI info for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").action(async(D)=>{if(!w0())return;let F=C("Fetching DOI info...").start();try{let $=await A2(D);if(F.stop(),console.log(),console.log(E.cyan(`DOI Information for ${D}:`)),console.log(`  Dataset Name:    ${$.name}`),console.log(),$.concept_doi){if(console.log(E.green("Concept DOI:")),console.log(`  DOI:  ${$.concept_doi}`),console.log(`  URL:  https://doi.org/${$.concept_doi}`),$.zenodo_concept_url)console.log(`  Zenodo: ${$.zenodo_concept_url}`)}else console.log(E.yellow("No concept DOI created yet")),console.log(E.gray("  Use 'nemar admin doi create' to create one"));if(console.log(),$.latest_version_doi){if(console.log(E.green("Latest Version DOI:")),console.log(`  DOI:  ${$.latest_version_doi}`),console.log(`  URL:  https://doi.org/${$.latest_version_doi}`),$.zenodo_latest_version_url)console.log(`  Zenodo: ${$.zenodo_latest_version_url}`)}else if($.concept_doi)console.log(E.yellow("No version DOI published yet")),console.log(E.gray("  Version DOIs are created automatically on PR merge"))}catch($){if($ instanceof u){if(F.fail($.message),$.statusCode===404)console.log(E.gray("  Dataset not found"));else if($.statusCode===403)console.log(E.gray("  This command requires admin privileges"))}else F.fail("Failed to fetch DOI info")}});n0.addCommand(R2);var T$=new D0("publish").description("Publication workflow management");T$.command("list").description("List publication requests").option("-s, --status <status>","Filter by status (requested, approving, published, denied)").addHelpText("after",`
+Dataset already has a concept DOI:`)),console.log(`  Concept DOI: ${E.cyan(X.concept_doi)}`),X.zenodo_concept_url)console.log(`  Zenodo URL:  ${X.zenodo_concept_url}`);return}}catch{}if(console.log(),console.log(E.cyan("Dataset Information:")),console.log(`  ID:          ${B.dataset_id}`),console.log(`  Name:        ${B.name}`),B.github_repo)console.log(`  GitHub:      ${B.github_repo}`);if(F.sandbox)console.log(`  Mode:        ${E.yellow("SANDBOX (test DOI)")}`);if(console.log(),F.sandbox)console.log(E.yellow("\u2501".repeat(60))),console.log(E.yellow.bold("                 SANDBOX MODE ENABLED")),console.log(E.yellow("\u2501".repeat(60))),console.log(E.yellow("  \u2022 Using Zenodo sandbox (sandbox.zenodo.org)")),console.log(E.yellow("  \u2022 DOI will NOT be indexed by DataCite")),console.log(E.yellow("  \u2022 DOI will NOT resolve in production")),console.log(E.yellow("  \u2022 Use this for testing workflows only")),console.log(E.yellow("\u2501".repeat(60))),console.log();console.log(E.red("WARNING: DOIs are PERMANENT and cannot be deleted!")),console.log(E.gray("The DOI will be pre-reserved but not published until the first version release.")),console.log();let J=F.sandbox?"Create TEST concept DOI on Zenodo SANDBOX?":"Create PERMANENT concept DOI on Zenodo PRODUCTION?",Q=await rD(J,F);if(Q!=="confirmed"){console.log(E.gray(Q==="declined"?"Skipped":"Cancelled"));return}let Y=C("Creating concept DOI on Zenodo...").start();try{let X=await Cv(D,{title:F.title,description:F.description,sandbox:F.sandbox});Y.succeed("Concept DOI created successfully");let G=C("Applying branch protection...").start();try{let H=await V$(D);if(H.warnings&&H.warnings.length>0){G.warn("Branch protection applied with warnings");for(let W of H.warnings)console.log(E.yellow(`  Warning: ${W}`))}else G.succeed("Branch protection applied")}catch(H){if(G.warn("Could not apply branch protection"),H instanceof u){if(console.log(E.gray(`  ${H.message}`)),H.statusCode===403)console.log(E.gray("  Check admin credentials and permissions"))}else console.log(E.gray(`  ${H instanceof Error?H.message:"Unknown error"}`));console.log(E.gray("  Manual setup: Go to GitHub repo Settings > Branches > Add rule"))}if(console.log(),console.log(E.green("DOI Information:")),console.log(`  Concept DOI: ${E.cyan(X.concept_doi)}`),console.log(`  Zenodo URL:  ${X.zenodo_url}`),console.log(),console.log(E.yellow("Next steps:")),console.log("  1. Set up automatic DOI publishing by running:"),console.log(E.gray(`     ${X.setup_command}`)),console.log("     (paste the webhook token when prompted)"),console.log(),console.log("  2. Update dataset_description.json with DatasetDOI field"),console.log("  3. Create a PR and merge it to trigger version DOI publication"),console.log(),F.sandbox)console.log(E.gray("Note: This is a sandbox DOI and will not resolve in production."))}catch(X){if(X instanceof u){if(Y.fail(X.message),X.statusCode===403)console.log(E.gray("  This command requires admin privileges"))}else Y.fail("Failed to create concept DOI"),console.log(E.gray(`  ${X instanceof Error?X.message:"Unknown error"}`))}});R2.command("info").description("Get DOI info for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").action(async(D)=>{if(!w0())return;let F=C("Fetching DOI info...").start();try{let $=await A2(D);if(F.stop(),console.log(),console.log(E.cyan(`DOI Information for ${D}:`)),console.log(`  Dataset Name:    ${$.name}`),console.log(),$.concept_doi){if(console.log(E.green("Concept DOI:")),console.log(`  DOI:  ${$.concept_doi}`),console.log(`  URL:  https://doi.org/${$.concept_doi}`),$.zenodo_concept_url){if(console.log(`  Zenodo: ${$.zenodo_concept_url}`),$.zenodo_concept_url.includes("sandbox.zenodo.org"))console.log(),console.log(E.yellow("Mode: SANDBOX (test DOI)")),console.log(E.yellow("  This DOI is not indexed by DataCite and will not resolve in production"))}}else console.log(E.yellow("No concept DOI created yet")),console.log(E.gray("  Use 'nemar admin doi create' to create one"));if(console.log(),$.latest_version_doi){if(console.log(E.green("Latest Version DOI:")),console.log(`  DOI:  ${$.latest_version_doi}`),console.log(`  URL:  https://doi.org/${$.latest_version_doi}`),$.zenodo_latest_version_url)console.log(`  Zenodo: ${$.zenodo_latest_version_url}`)}else if($.concept_doi)console.log(E.yellow("No version DOI published yet")),console.log(E.gray("  Version DOIs are created automatically on PR merge"))}catch($){if($ instanceof u){if(F.fail($.message),$.statusCode===404)console.log(E.gray("  Dataset not found"));else if($.statusCode===403)console.log(E.gray("  This command requires admin privileges"))}else F.fail("Failed to fetch DOI info")}});n0.addCommand(R2);var T$=new D0("publish").description("Publication workflow management");T$.command("list").description("List publication requests").option("-s, --status <status>","Filter by status (requested, approving, published, denied)").addHelpText("after",`
 Description:
   List all publication requests from users, with optional filtering by status.
   Shows dataset ID, status, requesting user, and current progress.
@@ -563,7 +563,7 @@ Examples:
   $ nemar sandbox           # Run sandbox training
   $ nemar sandbox status    # Check if training is completed
   $ nemar sandbox reset     # Reset for re-training
-`).action(MGD);async function MGD(){if(console.log(),console.log(E.bold("NEMAR Sandbox Training")),console.log(E.gray("Verify your setup and learn the upload workflow")),console.log(),!PD()){console.log(E.red("Not authenticated")),console.log(E.gray("Run 'nemar auth login' first"));return}let D=sD();if(D.sandboxCompleted){console.log(E.green("Sandbox training already completed!")),console.log(E.gray(`Dataset ID: ${D.sandboxDatasetId}`)),console.log(),console.log("You can upload real datasets with:"),console.log(E.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(E.gray("To re-run training, use: nemar sandbox reset"));return}console.log(E.bold("Step 1/6: Checking prerequisites..."));let F=C("Checking git-annex and SSH...").start(),$=await A$();if(!$.allPassed){F.fail("Prerequisites check failed"),console.log(),console.log(E.red("Missing requirements:"));for(let P of $.errors)console.log(E.yellow(`  - ${P}`));if(!$.githubSSH.accessible)console.log(E.gray("    Run 'nemar auth setup-ssh' to configure SSH"));return}F.succeed("All prerequisites met");let B=C("Verifying GitHub CLI authentication...").start(),J=await L$(D.githubUsername);if(!J.authenticated){B.fail("GitHub CLI not authenticated"),console.log(E.red(`  ${J.error}`)),console.log(),console.log("GitHub CLI is required for sandbox training. Install and authenticate:"),console.log(E.cyan("  brew install gh       # or visit https://cli.github.com/")),console.log(E.cyan("  gh auth login"));return}if(D.githubUsername&&!J.matches)B.warn("GitHub CLI user mismatch"),console.log(E.yellow(`  ${J.error}`)),console.log(),console.log("Your gh CLI is authenticated as a different GitHub account than your NEMAR account."),console.log("This may cause issues with repository access. To fix:"),console.log(E.cyan(`  gh auth login    # Login as ${D.githubUsername}`)),console.log(),console.log(E.yellow("WARNING: If upload fails with permission errors, this mismatch is the likely cause.")),console.log();else B.succeed(`GitHub CLI authenticated as ${J.username}`);console.log(),console.log(E.bold("Step 2/6: Generating test dataset..."));let Q=C("Creating minimal BIDS structure...").start(),Y;try{let P=Ky();Y=P.root;let VD=zy(P);Q.succeed(`Test dataset created (${C$(VD)})`),console.log(E.gray(`  Location: ${Y}`))}catch(P){Q.fail("Failed to generate test dataset"),console.log(E.red(`  ${P instanceof Error?P.message:"Unknown error"}`));return}console.log(),console.log(E.bold("Step 3/6: Registering sandbox dataset..."));let X=C("Creating dataset on NEMAR...").start(),G,H,W,K,V,A;try{let P=await z$({name:"Sandbox Training Dataset",description:"Placeholder dataset for sandbox training",files:[{path:"sub-01/eeg/sub-01_task-rest_eeg.edf",size:512000,type:"data"},{path:"dataset_description.json",size:200,type:"metadata"},{path:"participants.tsv",size:50,type:"metadata"},{path:"README",size:500,type:"metadata"},{path:"sub-01/eeg/sub-01_task-rest_eeg.json",size:300,type:"metadata"}],sandbox:!0});G=P.dataset.dataset_id,H=P.dataset.ssh_url,W=P.dataset.github_url,K=P.s3_config,V=P.dataset.s3_prefix,A=P.upload_urls||{},X.succeed(`Sandbox dataset created: ${E.cyan(G)}`),console.log(E.gray(`  GitHub: ${W}`)),await new Promise((VD)=>setTimeout(VD,1e4))}catch(P){if(X.fail("Failed to create sandbox dataset"),P instanceof u)console.log(E.red(`  ${P.message}`));else console.log(E.red(`  ${P instanceof Error?P.message:"Unknown error"}`));A1(Y);return}let Z=C("Accepting GitHub repository invitation...").start(),U=W?.match(/github\.com\/([a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+)/),L=U?U[1].replace(/\.git$/,""):null;if(!L){Z.fail("Invalid GitHub repository URL from backend"),console.log(E.red(`  Received: ${W||"(empty)"}`)),console.log(E.red("  Expected format: https://github.com/owner/repo")),console.log(),console.log("This may indicate a backend issue. Please contact support."),A1(Y);return}let M=await M$(L);if(M.accepted)if(M.alreadyCollaborator)Z.succeed("Already a collaborator on this repository");else Z.succeed("GitHub invitation accepted");else Z.warn("Could not auto-accept invitation"),console.log(E.yellow(`  ${M.error}`)),console.log(),console.log("You may need to accept the invitation manually:"),console.log(E.cyan(`  https://github.com/${L}/invitations`)),console.log();console.log(),console.log(E.bold("Step 4/6: Initializing repository..."));let w=C("Setting up git-annex...").start(),I=D.username&&D.email?{name:D.username,email:D.email}:void 0;try{await Z$(Y,{author:I}),await U$(Y),await N$(Y,H),w.succeed("Repository initialized")}catch(P){w.fail("Failed to initialize repository"),console.log(E.red(`  ${P instanceof Error?P.message:"Unknown error"}`)),A1(Y);return}if(console.log(),console.log(E.bold("Step 5/6: Uploading to S3...")),Object.keys(A).length===0)console.log(E.yellow("  No data files to upload (metadata only)"));else{let P=C("Uploading test data...").start();try{let yD=0,g=Object.keys(A).length,ED=await R$(Y,A,{jobs:4,onProgress:(WD)=>{if(WD.status==="completed"||WD.status==="failed")yD++,P.text=`Uploading... ${yD}/${g} files`}});if(ED.failed.length>0){P.fail(`Upload failed for ${ED.failed.length} file(s)`);for(let WD of ED.failed)console.log(E.red(`    Failed: ${WD}`));if(ED.error)console.log(E.red(`    Error: ${ED.error}`));console.log(),console.log(E.yellow("Sandbox training aborted due to upload failures.")),console.log(E.gray("Please check your network connection and try again.")),A1(Y);return}P.succeed(`Uploaded ${ED.uploaded} file(s)`)}catch(yD){P.fail("Upload failed"),console.log(E.red(`  ${yD instanceof Error?yD.message:"Unknown error"}`)),A1(Y);return}let VD=C("Registering file URLs...").start();try{let yD={};for(let ED of Object.keys(A))yD[ED]=`${K.public_url}/${V}/${ED}`;let g=await w$(Y,yD);if(!g.success){VD.fail(`URL registration failed for ${g.failed.length} file(s)`);for(let ED of g.failed)console.log(E.red(`    Failed: ${ED}`));console.log(),console.log(E.yellow("Sandbox training aborted due to URL registration failures.")),console.log(E.gray("This may indicate a git-annex configuration issue.")),A1(Y);return}VD.succeed(`Registered ${g.registered} file URLs`)}catch(yD){VD.fail("Failed to register URLs"),console.log(E.red(`  ${yD instanceof Error?yD.message:"Unknown error"}`)),A1(Y);return}}console.log(),console.log(E.bold("Step 6/6: Pushing to GitHub..."));let b=C("Saving and pushing...").start();try{await W5(Y,"Initial sandbox training upload",I),await E5(Y),b.succeed("Pushed to GitHub")}catch(P){b.fail("Failed to push to GitHub"),console.log(E.red(`  ${P instanceof Error?P.message:"Unknown error"}`)),A1(Y);return}let T=C("Finalizing...").start();try{await V$(G),await Ov(G),q0("sandboxCompleted",!0),q0("sandboxDatasetId",G),T.succeed("Sandbox training complete!")}catch(P){T.fail("Failed to finalize"),console.log(E.red(`  ${P instanceof Error?P.message:"Unknown error"}`)),A1(Y);return}A1(Y),console.log(),console.log(E.green.bold("Congratulations! Sandbox training completed successfully.")),console.log(),console.log("Your setup is verified and you're ready to upload real datasets:"),console.log(E.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(E.gray(`Sandbox dataset: ${G}`))}v$.command("status").description("Check sandbox training completion status").option("--refresh","Fetch latest status from server").action(async(D)=>{if(!PD()){console.log(E.red("Not authenticated")),console.log(E.gray("Run 'nemar auth login' first"));return}if(D.refresh){let F=C("Checking status...").start();try{let $=await Iv();if(q0("sandboxCompleted",$.sandbox_completed),$.sandbox_dataset_id)q0("sandboxDatasetId",$.sandbox_dataset_id);if(F.stop(),$.sandbox_completed){if(console.log(E.green("Sandbox training: Completed")),console.log(E.gray(`  Dataset ID: ${$.sandbox_dataset_id}`)),$.sandbox_completed_at)console.log(E.gray(`  Completed: ${$.sandbox_completed_at}`))}else console.log(E.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(E.cyan("  nemar sandbox"))}catch($){if(F.fail("Failed to check status"),$ instanceof u)console.log(E.red(`  ${$.message}`))}}else{let F=sD();if(F.sandboxCompleted)console.log(E.green("Sandbox training: Completed")),console.log(E.gray(`  Dataset ID: ${F.sandboxDatasetId}`));else console.log(E.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(E.cyan("  nemar sandbox"))}});v$.command("reset").description("Reset sandbox training status for re-training").option(_D,fD).option(tD,eD).action(async(D)=>{if(!PD()){console.log(E.red("Not authenticated")),console.log(E.gray("Run 'nemar auth login' first"));return}if(!sD().sandboxCompleted){console.log(E.yellow("Sandbox training not yet completed")),console.log(E.gray("Nothing to reset"));return}let $=await rD("Reset sandbox training status? 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+`).action(MGD);async function MGD(){if(console.log(),console.log(E.bold("NEMAR Sandbox Training")),console.log(E.gray("Verify your setup and learn the upload workflow")),console.log(),!PD()){console.log(E.red("Not authenticated")),console.log(E.gray("Run 'nemar auth login' first"));return}let D=sD();if(D.sandboxCompleted){console.log(E.green("Sandbox training already completed!")),console.log(E.gray(`Dataset ID: ${D.sandboxDatasetId}`)),console.log(),console.log("You can upload real datasets with:"),console.log(E.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(E.gray("To re-run training, use: nemar sandbox reset"));return}console.log(E.bold("Step 1/6: Checking prerequisites..."));let F=C("Checking git-annex and SSH...").start(),$=await A$();if(!$.allPassed){F.fail("Prerequisites check failed"),console.log(),console.log(E.red("Missing requirements:"));for(let P of $.errors)console.log(E.yellow(`  - ${P}`));if(!$.githubSSH.accessible)console.log(E.gray("    Run 'nemar auth setup-ssh' to configure SSH"));return}F.succeed("All prerequisites met");let B=C("Verifying GitHub CLI authentication...").start(),J=await L$(D.githubUsername);if(!J.authenticated){B.fail("GitHub CLI not authenticated"),console.log(E.red(`  ${J.error}`)),console.log(),console.log("GitHub CLI is required for sandbox training. 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To fix:"),console.log(E.cyan(`  gh auth login    # Login as ${D.githubUsername}`)),console.log(),console.log(E.yellow("WARNING: If upload fails with permission errors, this mismatch is the likely cause.")),console.log();else B.succeed(`GitHub CLI authenticated as ${J.username}`);console.log(),console.log(E.bold("Step 2/6: Generating test dataset..."));let Q=C("Creating minimal BIDS structure...").start(),Y;try{let P=Ky();Y=P.root;let VD=zy(P);Q.succeed(`Test dataset created (${C$(VD)})`),console.log(E.gray(`  Location: ${Y}`))}catch(P){Q.fail("Failed to generate test dataset"),console.log(E.red(`  ${P instanceof Error?P.message:"Unknown error"}`));return}console.log(),console.log(E.bold("Step 3/6: Registering sandbox dataset..."));let X=C("Creating dataset on NEMAR...").start(),G,H,W,K,V,A;try{let P=await z$({name:"Sandbox Training Dataset",description:"Placeholder dataset for sandbox training",files:[{path:"sub-01/eeg/sub-01_task-rest_eeg.edf",size:512000,type:"data"},{path:"dataset_description.json",size:200,type:"metadata"},{path:"participants.tsv",size:50,type:"metadata"},{path:"README",size:500,type:"metadata"},{path:"sub-01/eeg/sub-01_task-rest_eeg.json",size:300,type:"metadata"}],sandbox:!0});G=P.dataset.dataset_id,H=P.dataset.ssh_url,W=P.dataset.github_url,K=P.s3_config,V=P.dataset.s3_prefix,A=P.upload_urls||{},X.succeed(`Sandbox dataset created: ${E.cyan(G)}`),console.log(E.gray(`  GitHub: ${W}`)),await new Promise((VD)=>setTimeout(VD,1e4))}catch(P){if(X.fail("Failed to create sandbox dataset"),P instanceof u)console.log(E.red(`  ${P.message}`));else console.log(E.red(`  ${P instanceof Error?P.message:"Unknown error"}`));A1(Y);return}let Z=C("Accepting GitHub repository invitation...").start(),U=W?.match(/github\.com\/([a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+)/),L=U?U[1].replace(/\.git$/,""):null;if(!L){Z.fail("Invalid GitHub repository URL from backend"),console.log(E.red(`  Received: ${W||"(empty)"}`)),console.log(E.red("  Expected format: https://github.com/owner/repo")),console.log(),console.log("This may indicate a backend issue. 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 NEMAR is a curated repository for neurophysiology data in BIDS format.
 This CLI provides tools for uploading, downloading, and managing datasets.`).version(Ay,"-v, --version","Output the current version").option("--no-color","Disable colored output").option("--verbose","Enable verbose output").addHelpText("after",`

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nemar-cli",
-  "version": "0.3.7-dev.113",
+  "version": "0.3.7-dev.118",
   "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
   "type": "module",
   "main": "dist/index.js",